PMID- 20018063
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20111110
LR  - 20211020
IS  - 1753-6561 (Electronic)
IS  - 1753-6561 (Linking)
VI  - 3 Suppl 7
IP  - Suppl 7
DP  - 2009 Dec 15
TI  - Detecting significant single-nucleotide polymorphisms in a rheumatoid arthritis 
      study using random forests.
PG  - S69
AB  - Random forest is an efficient approach for investigating not only the effects of 
      individual markers on a trait but also the effect of the interactions among the 
      markers in genetic association studies. This approach is especially appealing for 
      the analysis of genome-wide data, such as those obtained from gene 
      expression/single-nucleotide polymorphism (SNP) array experiments in which the 
      number of candidate genes/SNPs is vast. We applied this approach to the Genetic 
      Analysis Workshop 16 Problem 1 data to identify SNPs that contribute to 
      rheumatoid arthritis. The random forest computed a raw importance score for each 
      SNP marker, where higher importance score suggests higher level of association 
      between the marker and the trait. The significance level of the association was 
      determined empirically by repeatedly reapplying the random forest on randomly 
      generated data under the null hypothesis that no association exists between the 
      markers and the trait. Using random forest, we were able to identify 228 
      significant SNPs (at the genome-wide significant level of 0.05) across the whole 
      genome, over two-thirds of which are located on chromosome 6, especially 
      clustered in the region of 6p21 containing the human leukocyte antigen (HLA) 
      genes, such as gene HLA-DRB1 and HLA-DRA. Further analysis of this region 
      indicates a strong association to the rheumatoid arthritis status.
FAU - Wang, Minghui
AU  - Wang M
AD  - Department of Epidemiology and Public Health, 60 College Street, Yale University 
      School of Medicine, New Haven, Connecticut 06520, USA. minghui.wang@yale.edu.
FAU - Chen, Xiang
AU  - Chen X
FAU - Zhang, Meizhuo
AU  - Zhang M
FAU - Zhu, Wensheng
AU  - Zhu W
FAU - Cho, Kelly
AU  - Cho K
FAU - Zhang, Heping
AU  - Zhang H
LA  - eng
GR  - R01 GM031575/GM/NIGMS NIH HHS/United States
GR  - R01 GM031575-28/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20091215
PL  - England
TA  - BMC Proc
JT  - BMC proceedings
JID - 101316936
PMC - PMC2795970
EDAT- 2009/12/19 06:00
MHDA- 2009/12/19 06:01
PMCR- 2009/12/15
CRDT- 2009/12/19 06:00
PHST- 2009/12/19 06:00 [entrez]
PHST- 2009/12/19 06:00 [pubmed]
PHST- 2009/12/19 06:01 [medline]
PHST- 2009/12/15 00:00 [pmc-release]
AID - 1753-6561-3-S7-S69 [pii]
AID - 10.1186/1753-6561-3-s7-s69 [doi]
PST - epublish
SO  - BMC Proc. 2009 Dec 15;3 Suppl 7(Suppl 7):S69. doi: 10.1186/1753-6561-3-s7-s69.